[gmx-users] Hydrogen bond occupancy for the dimer of Acetic Acid
Hi All. I'm trying to calculate the Hydrogen bond occupancy when there is two hydrogen bonds between same two acetic acid molecules at the same time. With g_hbond I can get the hbond.ndx giving me all ocuring hydrogen bonds group and the hbmap.xpm gives me the matrix of when these hydrogen bonds exist for each timeframe... How can I calculate the occupancy of when two hydrogen bonds exist between the same two molecules?? Best regards Rasmus -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Hydrogen bond occupancy for the dimer of Acetic Acid
Hi Rasmus, A simple solution would be to run g_hbond twice, with two separate groups for acetate 1 as donor and acetate 2 as acceptor or vice versa, check the existence an hydrogen bond with g_hbond -num and write a script to check when the two hydrogen bonds co-exist. Hope that helps, Ran. Rasmus Termo Lundsgaard wrote: Hi All. I'm trying to calculate the Hydrogen bond occupancy when there is two hydrogen bonds between same two acetic acid molecules at the same time. With g_hbond I can get the hbond.ndx giving me all ocuring hydrogen bonds group and the hbmap.xpm gives me the matrix of when these hydrogen bonds exist for each timeframe... How can I calculate the occupancy of when two hydrogen bonds exist between the same two molecules?? Best regards Rasmus -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Hydrogen bond occupancy for the dimer of Acetic Acid
Hi Ran. If I understand you right, then you suggest to have one molecule as acceptor, and the rest (499) as donors, and then look in the hbnum.xvg to see how often there is two hydrogen bonds... 1. is that I have to do this check for every molecule. 2. there is no guaranty that the two hydrogen bonds are to the same other molecule - it could very well be as a part of a chain... 3. If possible I would like to do measurement of distance between molecules when they are bonded as a dimer... Best regards Rasmus Ran Friedman wrote: Hi Rasmus, A simple solution would be to run g_hbond twice, with two separate groups for acetate 1 as donor and acetate 2 as acceptor or vice versa, check the existence an hydrogen bond with g_hbond -num and write a script to check when the two hydrogen bonds co-exist. Hope that helps, Ran. Rasmus "Termo" Lundsgaard wrote: Hi All. I'm trying to calculate the Hydrogen bond occupancy when there is two hydrogen bonds between same two acetic acid molecules at the same time. With g_hbond I can get the hbond.ndx giving me "all ocuring hydrogen bonds" group and the hbmap.xpm gives me the matrix of when these hydrogen bonds exist for each timeframe... How can I calculate the occupancy of when two hydrogen bonds exist between the same two molecules?? Best regards Rasmus -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Hydrogen bond occupancy for the dimer of Acetic Acid
Hi Rasmus, From your previous email I understood that you have only two molecules (you didn't write that you're using 500 and nothing on the rest of the system). Apparently, this is not the case. I don't think you can get what you want from g_hbond without modifying the source code. If you don't mind 500 runs you can use g_dist -dist, where group 1 is a single hydrogen bond donor oxygen and group two all potential acceptors, find the molecules which satisfy your criterion and then run g_hbond on them if you want to be sure that you have a hydrogen bond that satisfy angle criteria as well. Tedious, but can work with some scripting and patience. Ran. Rasmus Termo Lundsgaard wrote: Hi Ran. If I understand you right, then you suggest to have one molecule as acceptor, and the rest (499) as donors, and then look in the hbnum.xvg to see how often there is two hydrogen bonds... 1. is that I have to do this check for every molecule. 2. there is no guaranty that the two hydrogen bonds are to the same other molecule - it could very well be as a part of a chain... 3. If possible I would like to do measurement of distance between molecules when they are bonded as a dimer... Best regards Rasmus Ran Friedman wrote: Hi Rasmus, A simple solution would be to run g_hbond twice, with two separate groups for acetate 1 as donor and acetate 2 as acceptor or vice versa, check the existence an hydrogen bond with g_hbond -num and write a script to check when the two hydrogen bonds co-exist. Hope that helps, Ran. Rasmus Termo Lundsgaard wrote: Hi All. I'm trying to calculate the Hydrogen bond occupancy when there is two hydrogen bonds between same two acetic acid molecules at the same time. With g_hbond I can get the hbond.ndx giving me all ocuring hydrogen bonds group and the hbmap.xpm gives me the matrix of when these hydrogen bonds exist for each timeframe... How can I calculate the occupancy of when two hydrogen bonds exist between the same two molecules?? Best regards Rasmus -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
